To excavate the EST-SSR resourses of Ipomoea, 12812 non-redundant ESTs with the total length about 6.70 Mb were obtained by assembling 23406 ESTs from Ipomoea batatas (L.) Lam.Ipomoea batatas in NCBI. With the same way, 28422 unique sequences covering 17.19 Mb were generated from Ipomoea nil (L.) RothIpomoea nil. A total of 328 SSR loci for Ipomoea batatas with the the frequency of 2.56% and 962 SSR loci for Ipomoea nil with the frequency of 3.38% were identified by MISA. The EST-SSRs from Ipomoea batatas and Ipomoea nil had many common features. Among all the identified SSRs, dinucleotide repeats were dominant motifs and then were trinucleotide repeats. For dinucleotide repeats, AG/CT was the major motif, followed by AT/AT. And AAG/CCT was the most frequent motif among the trinucleotide repeats. The length of EST-SSRs was mainly distributed betweenn 20 bp to 22 bp. The result in the paper indicated that these EST-SSRs with abundant repeat motif types and high potential polymorphism have high value for exploitation and utilization.